Treating cancer with viral nucleic acid

ABSTRACT

This document provides methods and materials related to the use of nucleic acid coding for viruses to reduce the number of viable cancer cells within a mammal. For example, methods for using infectious nucleic acid to treat cancer, engineered viral nucleic acid, methods for making engineered viral nucleic acid, methods for identifying infectious nucleic acid for treating cancer, methods and materials for controlling virus-mediated cell lysis, and methods and materials for assessing the control of virus-mediated cell lysis are provided.

CROSS-REFERENCE TO RELATED APPLICATION(S)

This application is a continuation of U.S. application Ser. No.13/952,343, filed Jul. 26, 2013, which is a continuation of U.S.application Ser. No. 12/528,047, filed Dec. 21, 2009, which is aNational Stage application under 35 U.S. C. §371 of InternationalApplication No. PCT/US2008/054459, having a filing date of Feb. 20,2008, which claims priority to U.S. Application No. 60/902,200 filed onFeb. 20, 2007 and U.S. Application No. 61/009,968 filed on Jan. 4, 2008.The entire disclosure of these earlier applications are incorporatedherein by reference.

BACKGROUND

1. Technical Field

This document relates to methods and materials involved in treatingcancer with viral nucleic acid (e.g., nucleic acid coding for apicornavirus).

2. Background Information

The use of viruses to infect and kill cancer cells has been studied formany years. Typically, viruses known to infect and kill cancer cells arereferred to as oncolytic viruses. The use of oncolytic viruses in thistype of cancer therapy is generally different from their use in genetherapy. In gene therapy, a virus is primarily a delivery vehicle, usedto deliver a corrective gene or chemotherapeutic agent to a cancer cell.

SUMMARY

This document provides methods and materials related to the use ofnucleic acid coding for viruses to reduce the number of viable cancercells within a mammal. For example, this document provides methods forusing infectious nucleic acid to treat cancer, engineered viral nucleicacid, methods for making engineered viral nucleic acid, methods foridentifying infectious nucleic acid for treating cancer, methods andmaterials for controlling virus-mediated cell lysis, and methods andmaterials for assessing the control of virus-mediated cell lysis.

In general, one aspect of this document features a method for treatingcancer present in a mammal. The method comprises, or consistsessentially of, administering, to the mammal, an effective amount ofnucleic acid coding for a virus (e.g., a picornavirus) under conditionswherein cancer cells present within the mammal undergo cell lysis as aresult of synthesis of virus (e.g., picornavirus) from the nucleic acid,thereby reducing the number of viable cancer cells present within themammal. The mammal can be a human. The effective amount can be betweenabout 3×10¹⁰ and about 3×10″ virus genome copies. The picornavirus canbe a coxsackievirus. The cancer cells can be myeloma, melanoma, orbreast cancer cells. The nucleic acid can comprise, or consistessentially of, a microRNA target element comprising at least a regionof complementary to a microRNA present in non-cancer cells. A reducednumber of non-cancer cells present within the mammal can undergo celllysis as compared to the number of non-cancer cells that would undergocell lysis when the nucleic acid lacks the microRNA target element. ThemicroRNA can be a tissue-specific microRNA. The microRNA can be amuscle-specific, brain-specific, or heart-specific microRNA.

In another aspect, this document features an isolated nucleic acidcoding for a virus and comprising a microRNA target element having atleast a region that is complementary to at least a region of a microRNApresent in non-cancer cells and that is heterologous to the virus. Thevirus can be a picornavirus. The virus can be a coxsackievirus. Thevirus can be a poliovirus. The microRNA can be a tissue-specificmicroRNA. The microRNA can be a muscle-specific, brain-specific, orheart-specific microRNA.

In another aspect, this document features an isolated nucleic acidcoding for a virus and comprising a microRNA target element having atleast a region that is complementary to at least a region of acancer-specific microRNA and that is heterologous to the virus. Thenucleic acid, when administered to a mammal having cancer, can beexpressed in cancer cells. Expression of the nucleic acid can berestricted to cancer cells containing the cancer-specific microRNA whenthe nucleic acid is administered to a mammal having said cancer cells.

In another aspect, this document features a method of assessingcoxsackievirus-mediated cell lysis of non-cancer cells. The methodcomprises, or consists essentially of:

(a) administering nucleic acid coding for a coxsackievirus to a mammal,and

(b) determining whether or not the mammal develops myositis, paralysis,or death, wherein the presence of the myositis, paralysis, or deathindicates that the nucleic acid causes coxsackievirus-mediated celllysis of non-cancer cells, and wherein the absence of the myositis,paralysis, and death indicates that the nucleic acid lacks significantcoxsackievirus-mediated cell lysis of non-cancer cells. The mammal canbe a mouse. The nucleic acid can comprise a microRNA target element thatis complementary to a microRNA present in non-cancer cells or cancercells and that is heterologous to the coxsackievirus. The microRNA canbe a tissue-specific microRNA or a cancer-specific microRNA. ThemicroRNA can be a muscle-specific microRNA.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Although methods and materialssimilar or equivalent to those described herein can be used to practicethe invention, suitable methods and materials are described below. Allpublications, patent applications, patents, and other referencesmentioned herein are incorporated by reference in their entirety. Incase of conflict, the present specification, including definitions, willcontrol. In addition, the materials, methods, and examples areillustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and drawings, and from the claims.

DESCRIPTION OF THE DRAWINGS

FIG. 1 contains four line graphs plotting the TCID₅₀ value on H1-HeLacells for supernatant and cleared lysate samples collected from theindicated multiple myeloma cell line infected with CVA21 and culturedfor the indicated time.

FIG. 2 contains photographs of histological analysis of hind limb musclefor treated and untreated mice.

FIG. 3 contains two graphs plotting tumor volume at the indicated daysfor CVA21-treated (top) and untreated (bottom) mice.

FIG. 4 contains graphs plotting tumor volume at the indicated days formice treated intratumorally with the indicated amount of infectious RNAencoding a coxsackievirus.

FIG. 5 is a graph plotting tumor volume at the indicated days for micetreated intravenously with 50 μg of infectious RNA encoding acoxsackievirus.

FIG. 6 contains schematic diagrams of lentiviral transfer plasmidsencoding (A) eGFP tagged with four tandem copies of control ormuscle-specific microRNA target elements or (B) firefly luciferase.

FIG. 7 contains bar graphs plotting GFP (top) and luciferase (bottom)activity for non-muscle (HeLa, 3T3) and muscle (TE671, L6) cellstransduced with eGFP-encoding lentiviral vectors tagged with controlmicroRNA target elements (miR142-3p) or muscle-specific microRNA targetelements (miR133,miR-206,miR133/206) microRNA targets and non-taggedluciferase vectors. Top: Cells were grown in DMEM plus 10 percent FBSand harvested at 72 hours for flow analysis. Bottom: Cells were grown inDMEM plus 10 percent FBS and harvested at 72 hours for luciferase assay.

FIG. 8 contains bar graphs plotting GFP (top) and luciferase (bottom)activity for non-muscle (HeLa, 3T3) and muscle (TE671, L6) cellstransduced with eGFP-encoding lentiviral vectors tagged with controlmicroRNA target elements (miR142-3p) or muscle-specific microRNA targetelements (miR133,miR-206,miR133/206) microRNA targets and non-taggedluciferase vectors. Top: Cells were grown in differentiation medium thatincreases the expression of muscle-specific miRNAs and harvested forflow analysis of GFP expression. Bottom: Cells were grown indifferentiation medium that increases the expression of muscle-specificmiRNAs and harvested for luciferase assay.

FIG. 9 is a graph plotting percent inhibition of eGFP expression inmuscle cell lines versus averaged control cell lines.

FIG. 10 contains color photographs of phase contrast (upper) and GFPimmunofluorescence (lower) of 3T3 cells transduced with eGFP expressinglentiviral vectors tagged with control or muscle-specific microRNAtarget elements and grown in growth media.

FIG. 11 contains color photographs of phase contrast (upper) and GFPimmunofluorescence (lower) of HeLa cells transduced with eGFP expressinglentiviral vectors tagged with control or muscle-specific microRNAtarget elements and grown in growth media.

FIG. 12 contains color photographs of phase contrast (upper) and GFPimmunofluorescence (lower) of 293T cells transduced with eGFP expressinglentiviral vectors tagged with control or muscle-specific microRNAtarget elements and grown in growth media.

FIG. 13 contains color photographs of phase contrast (upper) and GFPimmunofluorescence (lower) of TE 671 cells transduced with eGFPexpressing lentiviral vectors tagged with control or muscle-specificmicroRNA target elements and grown in growth media.

FIG. 14 contains color photographs of phase contrast (upper) and GFPimmunofluorescence (lower) of L6 cells (rat myoblast) transduced witheGFP expressing lentiviral vectors tagged with control ormuscle-specific microRNA target elements and grown in growth media.

FIG. 15 contains color photographs of phase contrast (upper) and GFPimmunofluorescence (lower) of 3T3 cells transduced with eGFP expressinglentiviral vectors tagged with control or muscle-specific microRNAtarget elements and grown in differentiation media.

FIG. 16 contains color photographs of phase contrast (upper) and GFPimmunofluorescence (lower) of HeLa cells transduced with eGFP expressinglentiviral vectors tagged with control or muscle-specific microRNAtarget elements and grown in differentiation media.

FIG. 17 contains color photographs of phase contrast (upper) and GFPimmunofluorescence (lower) of TE 671 cells transduced with eGFPexpressing lentiviral vectors tagged with control or muscle-specificmicroRNA target elements and grown in differentiation media to inducehigher expression of muscle-specific miRNAs.

FIG. 18 contains color photographs of phase contrast (upper) and GFPimmunofluorescence (lower) of L6 cells (rat myoblast to myotube)transduced with eGFP expressing lentiviral vectors tagged with controlor muscle-specific microRNA target elements and grown in differentiationmedia.

FIG. 19 contains schematic diagrams of enterovirus and cardiovirusgenomes identifying examples of insertion sites for microRNA targetelements.

FIG. 20 is a schematic of RNA secondary structure of the 5′UTR of apicornavirus (Belsham and Sonnenberg; Microbiological Reviews, September1996, p. 499-511).

FIG. 21 is a schematic of RNA secondary structure of a virus containinga reverse complementarity region and a microRNA target element (modifiedfrom Belsham and Sonnenberg, 1996).

FIG. 22 is a schematic of the RNA of FIG. 21 with a 5′UTR conformationin the absence of miRNA.

FIG. 23 is a schematic of the RNA of FIG. 21 with a 5′UTR conformationin the presence of miRNA.

FIG. 24 is a schematic of the putative secondary structure of HepatitisC Virus 5′UTR containing miRT. Shaded area represents seed sequence towhich RISC can bind. (RNA secondary structure from Vienna RNA StructurePrediction Web Interface:http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi).

FIG. 25 is a schematic of the putative secondary structure of HepatitisC Virus 5′UTR lacking miRT. This schematic simulates these nucleotidesbeing unavailable for base pairing due to RISC binding.

FIG. 26 is a schematic of normal secondary structure of coxsackievirusA21 5′UTR.

FIG. 27 is a schematic of altered secondary structure of coxsackievirusA21 5′UTR with RC region introduced against stem loop 5 and insertion ofmiR155T.

FIGS. 28-31 are schematics of RNA secondary structure.

FIG. 32 is a schematic of coxsackievirus A21 genome and an alteredcoxsackievirus A21 genome.

FIG. 33 contains a schematic diagram of microRNA targeted CVA21 (A); onestep growth curves of WT, miRT, and RevT viruses in H1-HeLa cells (B),Mel 624 cells (C), Kas 6/1 cells (D), and H1-HeLa+miR-133 and miR-206mimics (E); a bar graph assessing viability 24 hrs. post viral infectionat MOI=1.0 with WT, miRT, or RevT CVA21 pretreated for 4 hrs. with 200nM miRNA mimics (F), a bar graph of viral titers collected 24 hrs. postinfection from supernatants of cells infected with WT, miRT, or RevTCVA21 in the presence of miRNA mimics (G), and a bar graph of in vitrosurvival of non muscle (H1-HeLa) or muscle (TE671) cells as determinedby MTT assay when transfected with 1 μg WT or miRT CVA21 RNA in 24 wellplates (H). *=p<0.01 from WT;*=<0.01 from miRNA control.

FIG. 34 contains three graphs plotting tumor volume at the indicateddays for SCID mice, which are carrying SQ multiple myeloma xenografts,that were treated with Opti-MEM control (A), 1×10⁶ WT CVA21 (B), and1×10⁶ miRT CVA21 (C); two Kaplan-Meier survival graphs of mice treatedwith 1 intratumoral dose of 1×10⁶ WT CVA21 or miRT CVA21 (D), or 1×10⁶WT CVA21, miRT CVA21, or RevT CVA21 (E); a graph of viral titerscollected from mice treated with WT or miRT CVA21 (F); and a sequencealignment of 3′NTR inserts from viruses collected from mouse #1-11 serumon day 45 (G).

FIG. 35 contains four graphs plotting tumor volume at the indicated daysfor SCID mice, which are carrying SQ Kas 6/1 xenografts, treated withOpti-MEM control (A), 1×10⁶ WT CVA21 (B), 1×10⁶ muscle specific miRTvirus (C), or 1×10⁶ revertant virus (D), and a Kaplan-Meier survivalcurve for control, WT CVA21, miRT virus, or revertant treated mice (E).

FIG. 36 contains three graphs plotting tumor volume at the indicateddays for SCID mice, which are carrying SQ Mel 624 melanoma xenografts,that were treated with Opti-MEM control (A), 1e6 WT CVA21 (B), or 1e6miRT CVA21 (C), and a Kaplan-Meier survival graph of control, WT CVA21,or miRT virus treated mice (D).

FIG. 37 contains a schematic diagram of lentiviral vector with revertanttarget (A), a sequence alignment of muscle specific miR-133/206T andRevertant virus (B), and a bar graph of GFP expression in cellstransduced at MOI=3.0 with lentiviral vectors containing hematopoeticcell specific miR-142-3p, muscle specific miR-133/206, and revertanttarget elements (C).

DETAILED DESCRIPTION

This document provides methods and materials related to the use ofnucleic acid coding for viruses to reduce the number of viable cancercells within a mammal. For example, this document provides methods forusing viral nucleic acid to reduce the number of viable cancer cellswithin a mammal. Nucleic acid coding for any appropriate virus can beused to reduce the number of viable cancer cells within a mammal. Insome cases, nucleic acid coding for a picornavirus can be used. Apicornavirus can be an enterovirus (e.g., bovine enterovirus, humanenterovirus A, human enterovirus B, human enterovirus C, humanenterovirus D, human enterovirus E, poliovirus, porcine enterovirus A,and porcine enterovirus B), a rhinovirus (e.g., human rhinovirus A andhuman rhinovirus B), a cardiovirus (e.g., encephalomyocarditis virus andtheilovirus), an apthovirus (e.g., equine rhinitis A virus andfoot-and-mouth disease virus), an hepatovirus (e.g., hepatitis A virus),a parechovirus (e.g., human parechovirus and ljungan virus), anerbovirus (e.g., equine rhinitis B virus), a kobuvirus (e.g., aichivirus), or a teschovirus (e.g., porcine teschovirus 1-7 and porcineteschovirus). In some cases, nucleic acid coding for a coxsackievirusA21 (Shafren et al., Clin. Cancer Res., 10(1 Pt. 1):53-60 (2004)),coxsackievirus B3 (Suskind et al., Proc. Soc. Exp. Biol. Med.,94(2):309-318 (1957)), poliovirus type III (Pond and Manuelidis, Am. J.Pathol., 45:233-249 (1964)), echovirus I (Shafren et al., Int. J.Cancer, 115(2):320-328 (2005)), or an encephalomyocarditis virus type E(Adachi et al., J. Neurooncol., 77(3):233-240 (2006)) can be used. Otherviruses having nucleic acid that can be used to reduce the number ofviable cancer cells can be identified using the screening methodsprovided in Example 1.

Other viruses having nucleic acid that can be used to reduce the numberof viable cancer cells include, without limitation, Adenoviridae virusessuch as mastadenoviruses (e.g., bovine adenovirus A, bovine adenovirusB, bovine adenovirus C, canine adenovirus, equine adenovirus A, equineadenovirus B, human adenovirus C, human adenovirus D, human adenovirusE, human adenovirus F, ovine adenovirus A, ovine adenovirus B, porcineadenovirus A, porcine adenovirus B, porcine adenovirus C, tree shrewadenovirus, goat adenovirus, guinea pig adenovirus, murine adenovirus B,murine adenovirus C, simian adenovirus, and squirrel adenovirus),aviadenoviruses (e.g., fowl adenovirus A, fowl adenovirus B, fowladenovirus C, fowl adenovirus D, fowl adenovirus E, goose adenovirus,duck adenovirus B, turkey adenovirus B, pigeon adenovirus),atadenoviruses (e.g., ovine adenovirus D, duck adenovirus A, bovineadenovirus D, possum adenovirus, bearded dragon, adenovirus, bovineadenovirus E, bovine adenovirus F, cervive adenovirus, chameleonadenovirus, gecko adenovirus, snake adenovirus), siadenoviruses (e.g.,frog adenovirus and turkey adenovirus A), and white sturgeonadenoviruses; Coronaviridae viruses such as coronaviruses (e.g. caninecoronavirus, feline coronavirus, human coronavirus 229E, porcineepidemic diarrhea virus, transmissible gastroenteritis virus, bovinecoronavirus, human coronavirus OC3, human enteric coronavirus, porcinehemagglutinating encephalomyelitis virus, puffinosis coronavirus, sarscoronavirus, infectious bronchitis virus, pheasant coronavirus, turkeycoronavirus, rabbit coronavirus) and toroviruses (e.g., bovinetorovirus, equine torovirus, human torovirus, and porcine torovirus);Flaviviridae viruses such as flaviviruses (e.g., gadgets gulley virus,kyasanur forest disease virus, langat virus, louping ill virus, omskhemorrhage fever virus, powassan virus, royal farm virus, tick-borneencephalitis virus, kadam virus, meadam virus, saumarez reef virus,tyuleniy virus, aroa virus, dengue virus, kedougou virus, cacipacorevirus, japanese encephalitis virus, koutango virus, murray valleyencephalitis virus, St. Louis encephalitis virus, usutu virus, west nilevirus, Yaounde virus, kokobera virus, bagaza virus, illheus virus,israel turkey meningoencephalomyelitis virus, ntaya virus, tembusuvirus, zika virus, banzi virus, bouboui virus, edge hill virus, jugravirus, saboya virus, sepik virus, uganda S virus, wesselsbron virus,yellow fever virus, entebbe bat virus, yokose virus, apoi virus, cowboneridge virus, jutiapa virus, modoc virus, sal vieja virus, san perlitavirus, bukalasa bat virus, carey island virus, Dakar bat virus, Montanamyotis leukoenchephalitis virus, phnom penh bat virus, rio bravo virus,cell fusing agent virus, and tamana bat virus), pestiviruses (e.g.,border disease virus, bovine viral diarrhea virus 1, bovine viraldiarrhea virus 2, classical swine fever virus, and pestivirus ofgiraffe), hepaciviruses (e.g., hepatitis C virus, GB virus B), GB virusA, and GB virus C; Hepadnaviridae viruses such as orthohepadnaviruses(e.g., hepatitis B virus, ground squirrel hepatitis B virus, woodchuckhepatitis B virus, woolly monkey hepatitis B virus, and arctic squirrelhepatitis virus) and avihepadnaviruses (e.g., duck hepatitis B virus);hepevirdae viruses such as hepeviruses (e.g., hepatitis E virus);Papillomaviridae viruses such as alphapapillomaviruses (e.g., humanpapillomavirus 32, human papillomavirus 10, human papillomavirus 61,human papillomavirus 2, human papillomavirus 26, human papillomavirus53, human papillomavirus 18, human papillomavirus 7, humanpapillomavirus 16, human papillomavirus 6, human papillomavirus 34,human papillomavirus 54, human papillomavirus cand90, humanpapillomavirus 71, and rhesus monkey papillomavirus),betapapillomaviruses (e.g., human papillomavirus 5, human papillomavirus9, human papillomavirus 49, human papillomavirus cand92, and humanpapillomavirus cand96), gammapapillomaviruses (e.g., humanpapillomavirus 4, human papillomavirus 48, human papillomavirus 50,human papillomavirus 60, and human papillomavirus 88),deltapapillomaviruses (e.g., european elk papillomavirus, deerpapillomavirus, ovine papillomavirus 1, and bovine papillomavirus 1),epsilonpapillomaviruses (e.g., bovine papillomavirus 5),zetapapillomaviruses (e.g., equine papillomavirus 1),etapapillomaviruses (e.g., fringella coelebs papillomavirus),thetapapillomaviruses (e.g, psittacus erithicus timneh papillomavirus),iotapapillomaviruses (e.g., mastomys natalensis papillomavirus),kappapapillomaviruses (e.g., cottontail rabbit papillomavirus and rabbitoral papillomavirus), lambdapapillomaviruses (e.g., canine oralpapillomavirus and feline papillomavirus), mupapillomaviruses (e.g.,human papillomavirus 1 and human papillomavirus 63), nupapillomaviruses(e.g., human papillomavirus 41), xipapillomaviruses (e.g., bovinepapillomavirus 3), omikronpapillomaviruses (e.g., phoecona spinipinnis),and pipapillomaviruses (e.g., hamster oral papillomavirus); Parvoviridaeviruses such as parvoviruses (e.g., chicken parvovirus, felinepanleukopenia virus, hb parvovirus, h-1 parvovirus, killham rat virus,lapine parvovirus, luiii virus, minute virus of mice, mouse parvovirus1, porcine parvovirus, rt parvovirus, tumor virus x, hamster parvovirus,rat minute virus 1, and rat parvovirus 1), erythroviruses (e.g., humanparvovirus b19, pig-tailed macaque parvovirus, rhesus macaqueparvovirus, simian parvovirus, bovine parvovirus type 3, and chipmunkparvovirus), dependoviruses (e.g., aav-1, aav-2, aav-3, aav-4, aav-5,avian aav, bovine aav, canine aav, duck aav, equine aav, gooseparvovirus, ovine aav, aav-7, aav-8, and bovine parvovirus 2),amdoviruses (e.g., aleutian mink disease virus), bocaviruses (e.g.,bovine parvovirus and canine minute parvovirus), densoviruses (e.g.,galleria mellonella densovirus, junonia coenia densovirus, diatraeasaccharalis densovirus, pseudoplusia includens densovirus, andtoxorhynchites splendens densovirus), iteraviruses (e.g., bombyx moridensovirus, casphalia extranea densovirus, and sibine fusca densovirus),brevidensoviruses (e.g., aedes aegypti densovirus and aedes albopictusdensovirus), and pefudensoviruses (e.g., periplaneta fuliginosadensovirus); Polyomaviridae viruses such as polyomaviruses (e.g.,african green monkey polyomavirus, baboon polyomavirus 2, bkpolyomavirus, bovine polyomavirus, budgerigar fledgling diseasepolyomavirus, hamster polyomavirus, human polyomavirus, jc polyomavirus,murine pneumotropic virus, murine pneumotropic virus, murinepolyomavirus, rabbit kidney vacuolating virus, simian virus 12, andsimian virus 40); Togaviridae viruses such as alphaviruses (e.g., auravirus, barmah forest virus, bebaru virus, cabassou virus, chikungunyavirus, eastern equine encephalitis virus, everglades virus, fort morganvirus, getah virus, highlands j virus, mayaro virus, middelburg virus,mosso das pedras virus, mucambo virus, ndumu virus, o′nyong-nyong virus,pixuna virus, rio negro virus, ross river virus, salmon pancreas diseasevirus, semliki forest virus, sindbis virus, southern elephant sealvirus, tonate virus, tonate virus, una virus, venezuelan equineencephalitis virus, western equine encephalitis virus, and whataroavirus), rubiviruses (e.g., rubella virus), and triniti virus;Arteriviridae viruses such as arteriviruses (e.g., equine arteritisvirus, lactate dehydrogenase-elevating virus, porcine reproductive andrespiratory syndrome virus, and simian hemorrhagic fever virus);Caliciviridae viruses such as vesiviruses (e.g., feline calicivirus,vesicular exanthema of swine virus, and san miguel sea lion virus),lagoviruses (e.g., european brown hare syndrome virus and rabbithemorrhagic disease virus), noroviruses (e.g., norwalk virus), andsapoviruses (e.g., sapporo virus); Retroviruses such as mammalian type B(e.g., mouse mammary tumor virus) and type C retroviruses (e.g., murineleukemia virus), Avian type C retroviruses (e.g., avian leukocis virus),type D retroviruses (e.g., squirrel monkey retrovirus, Mason-Pfizermonkey virus, langur virus, and simian type D virus), BLV-HTLVretroviruses (e.g., bovine leukemia virus), lentiviruses (e.g., bovine,equine, feline, ovinecaprine, and primate lentiviruses), andspumaviruses (e.g., simian foamy virus); and Astroviridae viruses suchas mamastroviruses (e.g., bovine astrovirus, feline astrovirus, humanastrovirus, ovine astrovirus, porcine astrovirus, and mink astrovirus)and avastroviruses (e.g., chicken astrovirus, duck astrovirus, andturkey astrovirus).

Nucleic acid coding for a virus can be administered directly to cancercells (e.g., by intratumoral administration) or can be administeredsystemically (e.g., by intravenous, intraperitoneal, intrapleural, orintra-arterial administration). The amount of nucleic acid administeredto a mammal can range from about 10 ng to about 1 mg (e.g., from 100 ngto 500 μg, from about 250 ng to about 250 μg, from about 500 ng to about200 μg, or from about 1 μg to about 100 μg) per kg of body weight. Insome cases, from about 100 ng to about 500 μg of nucleic acid coding fora virus can be administered as a single intratumoral dose. In somecases, the amount of nucleic acid administered to a mammal can be equalto a virus genome copy number of between about 3×10′ to about 3×10″genome copies (e.g., between about 3×10¹⁰ to about 3×10¹³, between about3×10¹⁰ to about 3×10¹², between about 3×10″ to about 3×10¹⁴, betweenabout 3×10″ to about 3×10¹³, or between about 3×10″ to about 3×10′²genome copies). For example, nucleic acid provided herein can beadministered in an amount such that about 3×10″ virus genome copies aredelivered to a mammal. In some cases, the amount of administered nucleicacid can be between about 3×10¹⁰ to about 3×10″ virus genome copies perkg of body weight.

Nucleic acid coding for a virus can contain sequences for eitherwild-type virus or for an engineered virus. For example, nucleic acidcoding for a wild-type coxsackievirus A21 virus can be used to reducethe number of viable cancer cells within a mammal. In some cases,nucleic acid coding for a virus can contain nucleic acid sequencesdesigned to control the expression of the viral polypeptides. Forexample, a nucleic acid provided herein can code for a virus and cancontain nucleic acid encoding a polypeptide (e.g., a single chainantibody polypeptide that binds to a target cell receptor) designed toalter the virus' cell specificity at the level of virus entry. In somecases, a nucleic acid provided herein can code for a virus and cancontain tissue-specific promoters to direct expression in desired cancercells.

As described herein, nucleic acid coding for a virus can be designed tocontain a microRNA target element (miRT) such that a correspondingmicroRNA (miRNA, specific miRNAs denoted as miR-#) present within anon-tumor cell can reduce virus gene expression, virus replication, orvirus stability in that non-tumor cell. MicroRNAs are small, 21-23nucleotide, highly conserved regulatory RNAs that can mediatetranslational repression or, in some cases, mRNA destruction byRISC-induced cleavage. MicroRNAs are present within many mammalian cellsand can have a tissue-specific tissue distribution. As such, microRNAscan be used to modulate the tropism of a replicating virus to provide atargeting approach for any virus. The ability of nucleic acid coding fora virus to result in non-tumor cell lysis can be reduced using amicroRNA target element having at least a region that is complementaryto a microRNA present in the non-tumor cells. For example,coxsackievirus A21 can infect muscle cells. Thus, microRNA targetelements that are complementary to microRNAs present in muscle cells canbe incorporated into coxsackievirus A21 nucleic acid to reduce musclecell lysis. Similarly, the safety of vaccines can be improved bymodulating the tropism of a virus. For example, a neuronal and/or brainmicroRNA target element can be incorporated into the polio virus toreduce the incidence of poliomyelitis induced by the oral polio vaccine.

This same approach can be used to reduce non-tumor cell lysis by otherviral nucleic acids. For example, microRNA target elements having atleast a region that is complementary to the microRNAs set forth in Table1 can be used to reduce cell lysis of the indicated tissue for thelisted viruses as well as for other viruses. Other examples of microRNAtarget elements that can be designed to reduce viral-mediated cell lysisinclude, without limitation, those having at least a regioncomplementary to a tissue-specific microRNA listed in Table 2. In somecases, nucleic acid provided herein can code for a virus and contain amicroRNA target element having at least a region complementary to aclassified tissue-specific microRNA. MicroRNA target elements can havecomplete complementarity to a microRNA. In some cases, a microRNA targetelement can contain mismatches in its complementarity to a microRNAprovided that it contains complete complementarity to a seed sequence(e.g., base pairs 2-7) of the microRNA. See, e.g., Lim et al., Nature,433(7027):769-73 (2005)).

TABLE 1 Silencing via incorporated microRNA target elements. VirusTissue microRNA Coxsackievirus A21 Muscle miR-1 Coxsackievirus A21Muscle miR-133 Coxsackievirus A21 Muscle miR-206 Coxsackievirus B3,Brain miR-101 Encephalomyocarditis-E Poliovirus III Echovirus ICoxsackievirus B3, Brain miR-124a,b Encephalomyocarditis-E PoliovirusIII Echovirus I Coxsackievirus B3, Brain miR-125 Encephalomyocarditis-EPoliovirus III Echovirus I Coxsackievirus B3, Brain miR-128Encephalomyocarditis-E Poliovirus III Echovirus I Coxsackievirus B3,Brain miR-131 Encephalomyocarditis-E Poliovirus III Echovirus ICoxsackievirus B3, Brain miR-132 Encephalomyocarditis-E Poliovirus IIIEchovirus I Coxsackievirus B3, Brain miR-134 Encephalomyocarditis-EPoliovirus III Echovirus I Coxsackievirus B3, Brain miR-135Encephalomyocarditis-E Poliovirus III Echovirus I Coxsackievirus B3,Brain miR-138 Encephalomyocarditis-E Poliovirus III Echovirus ICoxsackievirus B3, Brain miR-153 Encephalomyocarditis-E Poliovirus IIIEchovirus I Coxsackievirus B3, Brain miR-183 Encephalomyocarditis-EPoliovirus III Echovirus I Coxsackievirus B3, Brain miR-1b-2Encephalomyocarditis-E Poliovirus III Echovirus I Coxsackievirus B3,Brain miR-219 Encephalomyocarditis-E Poliovirus III Echovirus ICoxsackievirus B3, Brain miR-9 Encephalomyocarditis-E Poliovirus IIIEchovirus I Coxsackievirus B3, Brain miR-95 Encephalomyocarditis-EPoliovirus III Echovirus I Coxsackievirus B3, Brain miR-99bEncephalomyocarditis-E Poliovirus III Echovirus I Coxsackievirus B3,Heart miR-1 Echovirus I Coxsackievirus B3, Heart miR-133 Echovirus ICoxsackievirus B3, Heart miR-206 Echovirus I Coxsackievirus B3, HeartmiR-208 Echovirus I

TABLE 2 Classified tissue-specific microRNAs. miRNA Tissue SequenceReference miR-1 Muscle UGGAAUGUAAAGAAGUAUGUA Rao et al., Proc.(SEQ ID NO: 21) Nat'l. Acad. Sci., 103:8721-8726 (2006). miR-101 BrainUACAGUACUGUGAUAACUGAAG Lagos-Quintana et (SEQ ID NO: 22)al., Curr. Biol., 12:735-739 (2002). miR-122a LiverUGGAGUGUGACAAUGGUGUUUGU Fu et al., FEBS Lett., (SEQ ID NO: 23)579:3849-3854 (2005). miR- Brain UUAAGGCACGCGGUGAAUGCCALagos-Quintana et 124a,b (SEQ ID NO: 24) al., Curr. Biol.,12:735-739 (2002). miR-125 Brain UCCCUGAGACCCUUUAACCUGUGLiu et al., Proc. (SEQ ID NO: 25) Nat'l. Acad. Sci., 101:9740-9744(2004). miR- Digestive UCGUACCGUGAGUAAUAAUGC Shingara et al., RNA, 126AS(SEQ ID NO: 26) 11:1461-1470 (2005). miR-127 SpleenUCGGAUCCGUCUGAGCUUGGCU Lagos-Quintana et (SEQ ID NO: 27)al., Curr. Biol., 12:735-739 (2002). miR-128 BrainUCACAGUGAACCGGUCUCUUUC Liu et al., Proc. (SEQ ID NO: 28)Nat'l. Acad. Sci., 101:9740-9744 (2004). miR-130 LungCAGUGCAAUGUUAAAAGGGCAU Sempere et al., (SEQ ID NO: 29)Genome Biol., 5:R13 (2004). miR-132 Brain UAACAGUCUACAGCCAUGGUCGLagos-Quintana et (SEQ ID NO: 30) al., Curr. Biol., 12:735-739 (2002).miR-133 Muscle UUGGUCCCCUUCAACCAGCUGU Rao et al., Proc. (SEQ ID NO: 31)Nat'l. Acad. Sci., 103:8721-8726 (2006). miR-134 BrainUGUGACUGGUUGACCAGAGGG Schratt et al., (SEQ ID NO: 32)Nature, 439:283-289 (2006). miR-135 Brain UAUGGCUUUUUAUUCCUAUGUGASempere et al., (SEQ ID NO: 33) Genome Biol., 5:R13 (2004). miR-138Brain AGCUGGUGUUGUGAAUC Obernosterer et al., (SEQ ID NO: 34)RNA, 12:1161-1167 (2006). miR-142s Hematopoetic CAUAAAGUAGAAAGCACUACChen et al., Science, 5p, 3p (SEQ ID NO: 35) 303:83-86 (2004).UGUAGUGUUUCCUACUUUAUGGA (SEQ ID NO: 36) miR-143 DigestiveUGAGAUGAAGCACUGUAGCUCA Shingara et al., RNA, (SEQ ID NO: 37)11:1461-1470 (2005). miR-145 Digestive GUCCAGUUUUCCCAGGAAUCCCUUShingara et al., RNA, (SEQ ID NO: 38) 11:1461-1470 (2005). miR-148Liver, UCAGUGCACUACAGAACUUUGU Shingara et al., RNA, Stomach(SEQ ID NO: 39) 11:1461-1470 (2005). miR-15 B-cellUAGCAGCACAUAAUGGUUUGUG Calin et al., Proc. (Down- lymphocytic(SEQ ID NO: 40) Nat'l. Acad. Sci., regulated) leukemia 99:15524-15529(2002). miR-150 Spleen UCUCCCAACCCUUGUACCAGUG Shingara et al., RNA,(SEQ ID NO: 41) 11:1461-1470 (2005). miR-151 SpleenACUAGACUGAAGCUCCUUGAGG Sempere et al., (SEQ ID NO: 42)Genome Biol., 5:R13 (2004). miR-152 Liver UCAGUGCAUGACAGAACUUGGGSempere et al., (SEQ ID NO: 43) Genome Biol., 5:R13 (2004). miR-153Brain UUGCAUAGUCACAAAAGUGA Sempere et al., (SEQ ID NO: 44)Genome Biol., 5:R13 (2004). miR-155 Burkitt's UUAAUGCUAAUCGUGAUAGGGGMetzler et al., Genes Lymphoma (SEQ ID NO: 45) ChromosomesCancer, 39:167-169 (2004). miR-16 B-cell UAGCAGCACGUAAAUAUUGGCGCalin et al., Proc. (Down- lymphocytic  (SEQ ID NO: 46)Nat'l. Acad. Sci., regulated) leukemia 99:15524-15529 (2002). miR-17-5pLymphoma CAAAGUGCUUACAGUGCAGGUAGU He et al., Nature, (SEQ ID NO: 47)435:828-833 (2005). miR-181 Hematopoetic AACAUUCAACGCUGUCGGUGAGUChen et al., Science, (SEQ ID NO: 48) 303:83-86 (2004). miR-183 BrainUAUGGCACUGGUAGAAUUCACUG Sempere et al., (SEQ ID NO: 49)Genome Biol., 5:R13 (2004). miR-18a,b Lymphoma UAAGGUGCAUCUAGUGCAGAUAHe et al., Nature, (SEQ ID NO: 50) 435:828-833 (2005).UAAGGUGCAUCUAGUGCAGUUA (SEQ ID NO: 51) miR-192 KidneyCUGACCUAUGAAUUGACAGCC Sempere et al., (SEQ ID NO: 52)Genome Biol., 5:R13 (2004). miR-194 Kidney UGUAACAGCAACUCCAUGUGGASun et al., Nucleic (SEQ ID NO: 53) Acids Res., 32:e188 (2004). miR-195Hematopoetic UAGCAGCACAGAAAUAUUGGC Baskerville et al., (SEQ ID NO: 54)RNA, 11:241-247 (2005). miR-199 Liver CCCAGUGUUCAGACUACCUGUUCSempere et al., (SEQ ID NO: 55) Genome Biol., 5:R13 (2004). miR-19a,bLymphoma UGUGCAAAUCUAUGCAAAACUGA He et al., Nature, (SEQ ID NO: 56)435:828-833 (2005). UGUGCAAAUCCAUGCAAAACUGA (SEQ ID NO: 57) miR-204Kidney UUCCCUUUGUCAUCCUAUGCCU Sun et al., Nucleic (SEQ ID NO: 58)Acids Res., 32:e188 (2004). miR-204 Testis UUCCCUUUGUCAUCCUAUGCCUBaskerville et al., (SEQ ID NO: 59) RNA, 11:241-247 (2005). miR-206Muscle UGGAAUGUAAGGAAGUGUGUGG Rao et al., Proc. (SEQ ID NO: 60)Nat'l. Acad. Sci., 103:8721-8726 (2006). miR-208 HeartAUAAGACGAGCAAAAAGCUUGU Sempere et al., (SEQ ID NO: 61)Genome Biol., 5:R13 (2004). miR-212 Spleen UAACAGUCUCCAGUCACGGCCSempere et al., (SEQ ID NO: 62) Genome Biol., 5:R13 (2004). miR-215Liver AUGACCUAUGAAUUGACAGAC Sempere et al., (SEQ ID NO: 63)Genome Biol., 5:R13 (2004). miR-215 Kidney AUGACCUAUGAAUUGACAGACSun et al., Nucleic (SEQ ID NO: 64) Acids Res., 32:e188 (2004). miR-216Pancreas UAAUCUCAGCUGGCAACUGUG Sood et al., Proc. (SEQ ID NO: 65)Nat'l. Acad. Sci., 103:2746-2751 (2006). miR-219 BrainUGAUUGUCCAAACGCAAUUCU Sempere et al., (SEQ ID NO: 66)Genome Biol., 5:R13 (2004). miR-221 Hematopoetic AGCUACAUUGUCUGCUGGGUUUCFelli et al., Proc. (SEQ ID NO: 67) Nat'l. Acad. Sci., 102:1808118086 (2005). miR-222 Hematopoetic AGCUACAUCUGGCUACUGGGUCUCFelli et al., Proc. (SEQ ID NO: 68) Nat'l. Acad. Sci., 102:1808118086 (2005). miR-223 Hematopoetic UGUCAGUUUGUCAAAUACCCCChen et al., Science, (SEQ ID NO: 69) 303:83-86 (2004). miR-24 LungUGGCUCAGUUCAGCAGGAACAG Sempere et al., (SEQ ID NO: 70)Genome Biol., 5:R13 (2004). miR-25 Lymphoma CAUUGCACUUGUCUCGGUCUGAHe et al., Nature, (SEQ ID NO: 71) 435:828-833 (2005). miR-30b,c KidneyUGUAAACAUCCUACACUCAGCU Sempere et al., (SEQ ID NO: 72)Genome Biol., 5:R13 UGUAAACAUCCUACACUCUCAGC (2004). (SEQ ID NO: 73)miR-32 Lung UAUUGCACAUUACUAAGUUGC Sempere et al., (SEQ ID NO: 74)Genome Biol., 5:R13 (2004). miR-375 Pancreas UUUGUUCGUUCGGCUCGCGUGAPoy et al., Nature, (SEQ ID NO: 75) 432:226-230 (2004). miR-7 PituitaryUGGAAGACUAGUGAUUUUGUUG He et al., Nature, (SEQ ID NO: 76)435:828-833 (2005). miR-9 Brain UCUUUGGUUAUCUAGCUGUAUGASun et al., Nucleic (SEQ ID NO: 77) Acids Res., 32:e188 (2004). miR-95Brain UUCAACGGGUAUUUAUUGAGCA Babak et al., RNA, (SEQ ID NO: 78)10:1813-1819 (2004). miR-99b Brain CACCCGUAGAACCGACCUUGCGLiu et al., Proc. (SEQ ID NO: 79) Nat'l. Acad. Sci., 101:9740-9744(2004).

Common molecular cloning techniques can be used to insert microRNAtarget elements into nucleic acid coding for viruses. A nucleic acidprovided herein can contain one microRNA target element or multiplemicroRNA target elements (e.g., two, three, four, five, six, seven,eight, nine, ten, 15, 20, 25, 30, or more microRNA target elements). Forexample, a viral nucleic acid can contain microRNA target elementsinserted into both the 5′ and 3′ untranslated regions (UTR) in sectionswith limited secondary structure. In some cases, in the 5′UTR, microRNAtarget elements can be inserted upstream of the IRES. In some cases, inthe 3′UTR, microRNA target elements can be inserted adjacent to the stopcodon of a polypeptide or polyprotein. In some cases, microRNA targetelements can be inserted in an arrangement as shown in FIG. 19 or FIG.33A.

In some cases, microRNA target elements that are complementary tomicroRNAs that are ubiquitously expressed in normal cells with limitedexpression in tumor cells can be used to direct cell lysis to tumorcells and not non-tumor cells. For example, when using nucleic acidcoding for a virus to treat B-cell lymphocytic leukemia, the viralnucleic acid can be designed to contain microRNA target elementscomplementary to microRNAs that are ubiquitously expressed in normaltissue while being downregulated in B-cell lymphocytic leukemia cells.Examples of such microRNAs include, without limitation, miR-15 andmiR-16.

In some cases, a microRNA target element having at least a region ofcomplementarity to a cancer-specific microRNA can be used to direct celllysis to tumor cells. For example, nucleic acid coding for a virus caninclude microRNA target elements to direct microRNA-mediated targeting.Viruses such as picornaviruses (e.g., CVA21) can translate in acap-independent way. Namely, the viral Internal Ribosome Entry Site(IRES) can recruit transcription factors and ribosomes to the viral RNAwhere it is then translated. In addition, a cloverleaf structure on thetip of the 5′UTR can play a role in picornavirus replication (Barton etal., EMBO J., 20:1439-1448 (2001)). The following strategies aredesigned to conditionally distort the traditional secondary structureadopted by a virus (e.g., CVA21) in the 5′UTR in order to achieve atargeted oncolytic. These strategies are based, in part, upon RISCbinding to the viral genome, but causing little, or no, miRNA-mediatedcleavage. Rather, RISC in this situation has been manipulated to be amediator of steric hindrance as the targets introduced can lack completehomology required for RNA cleavage.

Strategy: Disruption of Viral IRES

By introducing binding elements of reverse complementarity to elementswithin the viral IRES (now called Reverse Complement “RC” region) atstem loops III, IV, and V, viral RNA can adopt a structure unlikely torecruit ribosomes (e.g., a malformed IRES), resulting in the inhibitionof viral translation. Then, by introducing an adjacent region containinga microRNA target element sequence between an RC region and a stem loopof the IRES to which the RC region is targeted, RISC recruitment by theendogenous microRNA to the introduced microRNA target element candisrupt the altered (engineered) secondary structure (FIG. 20).

Wild-type secondary structure can once again be adopted in the presenceof RISC, and a virus can be obtained that conditionally translates onlyin the presence of the microRNA whose target has been introduced intothe viral genome. With oncogenic miRNAs identified, expressedexclusively (or at least in much larger numbers) in neoplastic tissues,the resulting virus can be a tumor-specific oncolytic.

A reverse complement to part of stem loop V can be introduced upstreamin the 5′UTR (FIG. 21). In between engineered RC region and stem loop V,a micoRNA target element (miRT) can be inserted. With reference to FIG.21, the heavy gray line represents an engineered reverse complement,thin gray represents a microRNA target element, and the second heavygray line corresponds to the microRNA target element that can base pairwith the engineered reverse complement (note that this sequence need notbe altered, rather just the cognate for introduced sequence). Sincesequences can be designed such that Watson-Crick base pairing betweenthe two heavy gray sequences is more thermodynamically favored than thewild-type situation, a new stem loop can be preferentially formed unlessa factor is present to disrupt this new base pairing (i.e., RISC bindingto miRT).

In a normal cell, stem loop V can be altered due to base pairing betweenintroduced RC region (in gray), engineered to complement previous stemloop V. MicroRNA target element is shown in light gray, not bound byRISC as the target element is coding for a microRNA absent in thesecells. A new, inhibitory, loop can be formed in this situation (FIG.22).

In a cancer cell expressing a microRNA for an engineered microRNA targetelement, the microRNA whose target has been engineered into the viralgenome can bind RISC (FIG. 23). The association of RISC with this targetcan disrupt the aberrant base pairing, and the normal IRES structure canbe restored. This strategy can be used to disrupt loop III, IV, or V, orany combination thereof.

To construct nucleic acids for this strategy, unique restriction sitescan be introduced into a virus sequence (e.g., CVA 21 5′UTR) atlocations such as (a) upstream of stem loop III, (b) between stem loopsIII and IV, and/or (c) between stem loops IV and V. Combinations ofreverse complementary (RC) regions and microRNA target elements (miRTs)can be introduced into the new restriction sites. The RC regions can bedesigned against regions that are found in stem loops III, IV, or V,that are >7 bp in length, and that contain from 0-80% mismatch todetermine the optimal sequence able to be disrupted by RISC binding.MicroRNA target elements for any cancer-specific microRNA (e.g., twocancer-specific microRNAs such as miR-155 and miR-21) can be introducedadjacent to reverse complementary regions. These can contain fromnothing but seed sequence matches (e.g., base pairs 2-7) up to 100%homology.

Strategy: Disruption of 5′ Cloverleaf Motif

This strategy involves not disrupting binding of ribosomes to the IRES,but rather disrupting the 5′ cloverleaf (stem loops I, II in schematicpicture) found to be a cis-acting element required for picornavirusreplication. Hepatitis C Virus, a flavivirus, appears to require atarget sequence for a liver-specific microRNA in the 5′UTR of the viralgenome for viral accumulation in the liver (Jopling et al., Science,309:1577-1581 (2005)). The binding of RISC to its target element canallow a new secondary structure to be formed that mimics the5′cloverleaf formed in picornaviruses. The 5′UTR of Hepatitis C Virusis, in fact, more similar to picornaviruses than other flaviviruses inthat it lacks a 5′cap and translates utilizing a viral IRES. Thoughthere is little sequence homology between the Hepatitis C 5′UTR and thatof the picornaviruses, secondary structure analysis reveals that maskingthe sequence to which RISC binds causes the formation of a cloverleafstructure comparable to that of the picornaviruses (FIGS. 24-27).

The formation of the cloverleaf found in Coxsackievirus A21 can bedisrupted selectively by the inclusion of a microRNA target element inthis region, along with a sequence that can be reverse complementary toelements within the cloverleaf. In the absence of RISC binding,secondary structure can be altered, while in the presence of RISCbinding, it can assume wild-type base pairing.

Two different strategies can be use for the disruption of the 5′terminal cloverleaf motif:

A) Creation of Hepatitis C Virus/Coxsackievirus A21 5′UTR Chimera

1. Overlap Extension PCR to introduce miR-155T or miR-21T in place ofmiR-122T found in Hep C 5′UTR

2. PCR can be used to introduce portions Hepatitis C Virus 5′UTR intoCoxsackievirus A21

-   -   i) Portions of Hep C 5′UTR can be used in place of portions of        CVA21 5′UTR by (gray below represents Hepatitis C virus        contribution of cloverleaf motif) (FIG. 28).    -   ii) Hep C region can be introduced adjacent to engineered RC        region that complements portion of CVA cloverleaf motif (FIG.        29).

B) Insertion of RC Regions Up and Downstream of Cloverleaf

1. Unique restriction sites can be inserted before cloverleaf motifand/or after cloverleaf motif.

2. Disrupting Sequences (RC regions) and miRTs can be introduced intounique restriction sites.

i. in the case of insertion before cloverleaf motif, miRT can beadjacent to RC region on 3′ side (FIG. 30).

ii. in the case of insertion after cloverleaf motif, miRT can beadjacent to RC region on 5′ side (FIG. 31).

To construct nucleic acids for this strategy, reverse complementary (RC)regions can be designed against portions of cloverleaf motif, can be >7base pairs in length, and can contain from 0-80% mismatch to determinethe optimal sequence able to be disrupted by RISC binding. MicroRNAtarget elements for any cancer-specific microRNA (e.g., twocancer-specific microRNAs such as miR-155 and miR-21) and for controlmicroRNA can be introduced adjacent to RC regions. These can containfrom nothing but seed sequence matches (e.g., base pairs 2-7) up to 100%homology.

Screening Strategy:

In order to screen the candidates obtained, a system can be used wherebythe capsid proteins VP1, VP2, and VP3 are replaced by the luciferasegene (FIG. 32). In polioviruses, this system can retain the enzymaticactivity of luciferase (Porter et al., Virology, 243:1-11 (1998)). Inthis strategy, cancer-specific miRNAs miR-155 and miR-21 can be used forscreening purposes to determine possible secondary structures that causetranslation in the presence and translational inhibition in absence ofthese miRNAs. These are not intended to be limiting, but rather, can beused as tools to screen secondary structure.

1. Construction of stable cell line expressing cancer-specific microRNA

Briefly, HeLa cells can be transduced with lentiviral vector expressingmiR-155, miR-21, or control pri-miRNA sequence driven by a Pol IIpromoter. Endogenous cellular processing pathway by Drosha and Dicerresult in expression of mature siRNAs analogous to mature microRNAs.Note that these cell lines can be engineered to express thesepseudo-miRNAs and endogenous forms of these specific miRNAs are notexpressed.

2. Transfection of engineered viral RNA in control & miR-155 and miR-21expressing cells

RNA can be isolated from clones from the above strategies using Ambionin vitro Maxiscript transcription kit. RNA can be transfected with MinisTrans-IT mRNA transfection kit into control and cancer-specific microRNAexpressing HeLa cell lines.

3. Luciferase Assay

Luciferase assay can be performed on cell lines 1-72 hours posttransfection. Positive response can be measured by a 3 fold higherproduction of luciferase in miR-155 or miR-21 expressing cell lines overcontrol miRNA expressing lines.

To screen for putative tumor-specific oncolytics, the above assay canprovide an artificial method of simulating the microRNA pathway. Use oflentiviral vectors to express siRNAs that mimic microRNAs, however, canexpress these small regulatory RNAs in higher copy number than areexpressed in the cancers. The following can be a protocol to screenobtained oncolytics in the presence of microRNAs expressed in variouscopy numbers.

4. Testing for CPE with WT CVA21 in miR-155 and miR-21 expressing celllines

After titration on suitable cell line, 1.0 TCID₅₀/cell can be added andCPE determined 48 hours post infection by MTT assay on cell linesexpressing miR-155 (e.g., Raji, OVI-Ly3, L428, KMH2, L1236, and L591)and cells lines expressing miR-21 (e.g., U373, A172, LN229, U87, LN428,LN308).

CPE of >90% can correspond to a cell line that can be used in theanalysis of previously identified, putative, tumor-specific oncolytics.

5. Transfection of viral RNA in identified cell line from above eithercontaining antisense 2′O-methyl oligoribonucleotides (2′OMe) againstmiR-155, miR-21, or ubiquitous miRNA

The addition of antisense 2′OMe-RNA can be used to inactivatespecifically its cognate microRNA (Meister et al., RNA, 10:544-550(2004)). Using this strategy, cell lines that specifically inactivatethe activity of endogenously expressed miRNAs (in wild type copynumbers) can be obtained and used to show efficacy in this system.

6. Luciferase Assay

Luciferase assay can be performed on cell lines in the absence/presenceof antisense 2′OMe-miR-155 or antisense 2′OMe-miR-21. Positive responsescan be measured by a 3 fold higher production of luciferase in theabsence of antisense 2′OMe-miR-155 or antisense 2′OMe-miR-21 inexpressing cell lines over luciferase production in the presence ofantisense 2′OMe-miR-155 or antisense 2′OMe-miR-21.

7. Insertion Sequences cloned into wild-type CVA-21

Identified insertion sequences that elicited a positive response in bothlentiviral vector expression screening and using 2′O-methyloligoribonucleotides can be cloned back into capsid-expressingCoxsackievirus A21. New microRNA target elements can be inserted inplace of miR-155 or miR-21 used for screening purposes.

8. Screening via INA Screening Assay

The methods and materials provided herein can be used to screen foroncolytic activity. The obtained viruses can be propagated in thepresence of miR-155, miR-21 or other inserted oncogenic microRNA targetelements.

Examples of cancer-specific microRNAs include, without limitation, thoselisted in Table 3.

TABLE 3 Cancer-specific microRNAs. microRNA Cancer miR-25 LymphomamiR-21 Glioblastoma (+/− Breast Cancer) miR-19a,b Lymphoma miR-18a,bLymphoma miR-17-5p Lymphoma miR-155 Burkitt's Lymphoma

When assessing nucleic acid for the ability to reduce the number ofviable cancer cells within a mammal, any appropriate cancer model can beused. For example, a SCID mouse model containing implanted tumor cellssuch as those listed in Table 4 can be used.

TABLE 4 Tumor model cell lines. Cancer Tumor Type Cell Line Breast HumanXenograft BT-474 Breast Human Xenograft MCF7/S Breast Human XenograftMCF7/TAMR-1 Breast Human Xenograft MCF7/Mitox Breast Human XenograftMCF7/D40 Breast Human Xenograft MDA-MB-231 Breast Human XenograftMDA-MB-435 Breast Human Xenograft ZR-75-1 Breast Human Xenograft ACC3199Breast Human Xenograft T-47D Cervix Human Xenograft HeLa Cervix HumanXenograft Ca Ski Cervix Human Xenograft SiHa Cervix Human XenograftC-33A Colon Human Xenograft CaCo-2 Colon Human Xenograft HCA-7 ColonHuman Xenograft HCT 116 Colon Human Xenograft HT-29 Colon HumanXenograft SW480 Colon Human Xenograft SW620 Colon Human Xenograft DLD-1Colon Human Xenograft LoVo Colon Mouse Allograft CT26.WT FibrosarcomaHuman Xenograft HT-1080 Glioblastoma Human Xenograft U-87 MGGlioblastoma Human Xenograft SF 767 Leukemia Human Xenograft HL-60,Leukemia Human Xenograft K562/S Leukemia Human Xenograft K562/MDRLeukemia Human Xenograft KG-1 Leukemia Human Xenograft OCI-AML3 LeukemiaTumor Supressor KO NF-1 Mutant Liver Human Xenograft SK-HEP-1 LiverHuman Xenograft HC-4 Liver Human Xenograft HepG2 Liver Human XenograftHep 3B Lung Human Xenograft A549 Lung Human Xenograft MV522 Lung HumanXenograft NCI-H1299 Lung Human Xenograft NCI-H460 Lung Human XenograftNCI-H1975 Lung Mouse Allograft PC-6 Lung Mouse Allograft LL/2 Lung HumanXenograft NCI-H69/S Lung Human Xenograft H69AR Lung Human XenograftSHP-77 Lung Human Xenograft DMS 53 Lung Human Xenograft DMS 153 LungHuman Xenograft DMS 114 Lymphoma Human Xenograft Daudi Lymphoma HumanXenograft OCILY8 Lymphoma Human Xenograft Raji Lymphoma Human XenograftGranta 519 Lymphoma Human Xenograft Granta 4 Lymphoma Human XenograftKARPAS-299 Lymphoma Human Xenograft CA46 Lymphoma Human Xenograft U937Lymphoma Human Xenograft H33HJ-JA1 Melanoma Human Xenograft A-375Melanoma Human Xenograft DH903 Melanoma Human Xenograft JH1308 MelanomaHuman Xenograft KD1592 Melanoma Human Xenograft PS1273 Melanoma HumanXenograft WM1791C Melanoma Human Xenograft LOX IMVI Melanoma HumanXenograft SBL2 Melanoma Mouse Allograft B16-F0 Melanoma Human XenograftSK-MEL-5 Myeloma Human Xenograft 8226/S Myeloma Human Xenograft 8226/VMyeloma Human Xenograft 8228/Dox40 Myeloma Human Xenograft ARH-77Myeloma Human Xenograft ARHD60 Myeloma Human Xenograft Kas-6/1 MyelomaHuman Xenograft KMM-1 Neuroblastoma Human Xenograft SK-N-SH OsteosarcomaHuman Xenograft Saos-2 Osteosarcoma Human Xenograft U-2 OS Ovarian HumanXenograft A2780 Ovarian Human Xenograft OVCAR-3 Ovarian Human XenograftSK-OV-3 Ovarian Human Xenograft IGROV1 Ovarian Human Xenograft OV202Pancreatic Human Xenograft AsPC-1 Pancreatic Human Xenograft BxPC-3Pancreatic Human Xenograft CFPAC-1 Pancreatic Human Xenograft HPAF-IIPancreatic Human Xenograft MIA PaCa-2 Pancreatic Human Xenograft PANC-1Pancreatic Human Xenograft SU.86.86 Pancreatic Human Xenograft Capan-2Prostate Human Xenograft DU 145 Prostate Human Xenograft LNCaP ProstateHuman Xenograft PC-3 Renal Human Xenograft A-498 Renal Human XenograftACHN Renal Human Xenograft 786-O Renal Human Xenograft Caki-1 StomachHuman Xenograft KATO III Uterine Human Xenograft RL 95.2 Uterine HumanXenograft MES-SA

The invention will be further described in the following examples, whichdo not limit the scope of the invention described in the claims.

EXAMPLES Example 1 Screening for Infectious Nucleic Acid that can beUsed to Treat Cancer

The following screening assay is used to identify infectious nucleicacid that can be used to treat cancer. First, virus particles areobtained and assessed in vitro using a lysis assay performed with humancancer cells. Briefly, after titrating virus particles on a suitablecell line, 1.0 TCID₅₀/cell of virus particles is added to a panel ofhuman cancer cell lines, and the cytopathic effect (CPE) is measured 48hours post infection using an MTT assay as described elsewhere((Mossman, J. Immunol. Methods, 65:55-63 (1983)). Viruses that exceed aCPE of >90 percent for any particular cell line are considered asputative oncolytics and proceed to in vivo screening in rodent models.

The following is performed to assess in vivo oncolytic effects. Briefly,SCID mice are inoculated with 10⁶ cancer cells (e.g., a cancer cell linelisted in Table 4). When tumors reach 0.5 cm in diameter, putativeoncolytic viruses are inoculated into the mice at low dose (e.g., 10³TCID₅₀ for intratumoral injections; 10⁴ TCID₅₀ for intravenousinjections; or 10⁵ TCID₅₀ for intraperitoneal injections). The tumorsare measured to determine whether or not the administered virus caused areduction in tumor size. Viruses that cause tumor reduction within twoweeks are then screened by direct injection of viral nucleic acid.

To assess the direct injection of viral nucleic acid, tumors areestablished in SCID mice as above. Then, 1, 2, 4, 8, 16, and 32 μg ofviral nucleic acid is intratumorally injected in a total volume of 100μL of OptiMEM® (a chemically-defined medium; Invitrogen™). The titer ofvirus within serum is determined after seven days. A positive responseis achieved when a titer of virus particles in serum is equal to orgreater than 10³ TCID₅₀ and an overall reduction of tumor size that isgreater than 30 percent.

Example 2 Multiple Myeloma Cells are Highly Susceptible toCoxsackievirus Infection

Coxsackievirus A21 (CVA21; Kuykendall strain) was purchased from ATCC.CVA21 was propagated on H1-HeLa cells (ATCC) by plating cells at 75percent confluence 24 hours prior to infection. Cells were infected withCVA21 at MOI 0.1 for two hours at 37° C. Unincorporated virus wasremoved by replacing the growth media. Infected cells were checkedregularly over 48 hours for CPE. When 90 percent of cells had detached,the remaining cells were scraped from the flask, and the cell pellet washarvested. These cells were then resuspended in one to two mL ofOptiMEM® (Invitrogen) and subjected to three freeze-thaw cycles. Celldebris was removed by centrifugation, and the cleared cell lysatecontaining virus was aliquoted and stored at −80° C.

Titration of CVA21 was performed on H1-HeLa cells. Cells were plated in96 well plates at 50 percent confluence. After 24 hours, serial ten-folddilutions (−2 to −10) were made of the virus; 100 μL of each dilutionwas added to each of eight duplicate wells. Following incubation at 37°C. for 72 hours, wells were fixed and stained (0.1% crystal violet, 20%methanol, 4% paraformaldehyde). Wells were then accessed for CPEmanifest as non-staining areas devoid of viable cells. If purplestaining cells were seen on 75 percent or less of the well surface, thenthe well was scored positive. TCID₅₀ values were determined using theSpearman and Kärber equation.

One-step growth curves were performed using four multiple myeloma celllines (JJN-3, KAS6/1, MM1, ARH-77). Each cell line was incubated withCVA21 at a MOI of 3.0 for 2 hours at 37° C. Following this incubation,cells were centrifuged, and unincorporated virus was removed. Cells wereresuspended in fresh growth media and plated in 24 well plates witheight wells for each cell line tested. At predetermined time-points (2,4, 6, 12, 24, 36, 48, and 72 hours), cells and growth media wereharvested from one well for each cell line. Cells were separated fromgrowth media (supernatant) with fresh growth media being added to cellpellet. Both fractions were frozen at −80° C.

At the completion of all time-points, the samples were thawed, and thecell pellets were cleared from the samples by centrifugation providing acleared cell lysate fraction and a media supernatant fraction. The titerwas determined for both fractions.

All myeloma cell lines exhibited rapid and high titer propagation ofCVA21 with three of the four cell lines approaching plateau by 12 hourswith titers as high as 10⁷ to 10⁸ TCID₅₀ per mL (FIG. 1). All titersremained steady out to the 72 hour time point. These results demonstratethat multiple myeloma cell lines are highly susceptible to CVA21infection and rapidly propagate this virus.

Example 3 Coxsackievirus-Mediated Tumor Regression is Associated withViremia and Myositis

An in vivo study was completed in SCID mice. Mice were irradiated (150cGy) 24 hours prior to the subcutaneous implantation of 10⁷ KAS6/1 cellsinto the right flank. When tumors reached an average size of 0.5 cm,mice were treated with two injections (48 hours apart) of CVA21, each5.6×10⁵ TCID₅₀. The mice were divided into three groups, Opti-MEMcontrol (no virus), intratumoral (IT) delivery, and intravenous (IV)delivery. Tumors began regressing by day 8 at which time the mice begandragging their hind limbs. Over the next 48 hours, the mice wasted andbecame weak being unable to reach food or water due to progressive limbweakness. At around day 10, the mice either died or had to beeuthanized. In all treated mice, the pattern was the same: tumorregression coincided with hind limb paralysis followed by wasting andeuthanasia or death.

Mouse tissue was harvested and applied to a monolayer of H1-HeLa cellsto check for recovery of live virus from tissues. The control mousetissues exhibited no CPE. With virus treated mice, virus was recoveredfrom residual tumor tissue as well as from adjacent and distant skeletalmuscle tissue. Other tissues including heart, brain, liver, and spleenwere negative (Table 5).

TABLE 5 CPE of mouse tissue overlays on H1-HeLa cells Mice Tumor LiverSpleen Brain Muscle IV virus #1 +++ − − − ++ IV virus #2 +++ − − − ++ IVvirus #3 +++ − − − ++ IT virus #1 +++ − − − ++ No virus #1 − − − − −Viral recovery was considered negative (−) if no CPE was observed by 96hrs. (++) denotes >50% CPE observed within 24 hrs. (+++) denotes >50%CPE observed within 12 hrs

In another in vivo study, mice were euthanized at the time point oftumor regression/hind limb paralysis, and their tissues prepared forhistological examination. The pathology results indicated thatvirus-treated mice had significant myositis in their hind limb muscles(FIG. 2).

The analysis of tumor volume revealed regression of all tumors treatedwith one intratumoral dose of CVA21 (FIG. 3). By day 7, tumors wereregressing, and mice exhibited signs of hind limb paralysis associatedwith viremia causing myositis. All treated mice were dead by day 10,while control mice had big tumors but were otherwise healthy. Blooddrawn from treated mice three and seven days post treatment exhibitedtiters of CVA21 that ranged from 3×10⁵ to 3×10⁶ per mL (Table 6).

TABLE 6 Serum titers of CVA21 in treated and control mice (TCID₅₀)Control mice CVA21 treated mice 72 hours post treatment 0 ± 0 1.08e6 ±3.15e5 1 week post treatment 0 ± 0 3.16e6 ± 0

As described above, the effect of CVA21 on multiple myeloma cell linesand xenografts was examined. CVA21 was propagated and titered on H1-HeLacells. FACScan analysis was performed with human multiple myeloma celllines (KAS6/1, MM1, JJN-3, ARH-77). All the cell lines tested were foundto express surface receptors for both DAF and ICAM-1, making them viablecandidates for CVA21 infection. The in vitro studies revealed that celllines incubated with decreasing amounts of CVA21 exhibit rapidcytopathic effect in doses as low as MOI=0.0014 for three of the celllines tested (dose for CPE with JJN-3 was MOI=0.028). With in vivostudies in SCID mice bearing human myeloma xenografts, tumors quicklyand completely responded to CVA21 (both IV and IT administration). Aspromptly as the tumors regressed, the mice became sick with hind-limbparalysis and quickly died. Pathology reports revealed complete ablationof all tumor tissue but also signs of widespread myositis in muscletissues. CVA21 virus was recovered from muscle biopsies but there was noevidence of CNS infection. Toxicity was observed in tumor bearinganimals with a CVA21 dose as low as 560 TCID₅₀. In an attempt toameliorate the myositis, adenoviruses coding for mouse IFNγ wasadministered prior to CVA21 therapy. Blood levels of IFNγ were measuredby ELISA and were 1500-3000 pg/mL compared to 150 pg/mL in untreatedcontrol mice. There was little impact on tumor response or survival.These results demonstrate that CVA21 can be a potent anti-myeloma agent.

Example 4 Low Doses of Coxsackievirus Cause Tumor Regression

Four tumor bearing mice (KAS6/1 tumor cells) were treated byintratumoral injections with low dose CVA21: two mice with 5,600 TCID₅₀and two mice with 560 TCID₅₀. By day 6, all of the treated tumors begangetting soft and started regressing. Between days 7-9, all miceexhibited signs of virema with hind limb paralysis and wasting. At thispoint, all mice met the sacrifice criteria and were euthanized by day12.

Example 5 Infectious RNA Encoding a Coxsackievirus Causes TumorRegression, Viremia, and Myositis

CVA21 infectious RNA was synthesized by in vitro transcription of aCVA21 plasmid DNA (obtained from Eckhard Wimmer). The CVA21 DNA waslinearized by cutting with Mlu 1 restriction enzyme upstream of the T7promoter site. This digest was terminated by ethanol precipitation. Thetranscription reaction was then assembled using the Ambion (Austin,Tex.) MEGAscript® kit. Briefly, the linearized DNA was mixed withreaction buffer, ribonucleotide solutions, and enzyme. Transcription wasallowed to proceed at 37° C. for three hours. The sample was thentreated with DNase 1 to remove the template DNA. Ambion's MEGAc1ear™purification kit was used to purify the RNA for in vitro or in vivostudies. CVA21 RNA samples were quantitated by UV absorbance. The purityand size of the transcription product were assessed by formaldehyde gelelectrophoresis. Activity of the CVA21 transcript was assessed bytransfecting RNA into H1-HeLa cells using the Minis (Madison, Wis.)TranIT®-mRNA Transfection Kit and monitoring cells for CPE and forrelease of titratable CVA21 virus.

To test the effectiveness of CVA21 infectious RNA to cause the sametumor destruction as CVA21 virus, SCID mice bearing KAS6/1 subcutaneousxenografts were given intratumoral injections of CVA21 RNA at increasingdoses (0, 1 μg, 2 μg, 4 μg, 8 μg, 16 μg, and 32 μg). Tumors weremeasured daily, and mice were monitored for signs of hind limbparalysis. Blood was also drawn from mice at days 3, 7, 10, 14, 17, and21 to monitor serum titers of CVA21 virus. All mice in the groups thatreceived 4 μg or more of RNA had tumor regression, viremia, and myositiscausing hind limb paralysis and death (Table 7 and FIG. 4). Two mice ineach of the 1 μg and 2 μg groups exhibited tumor regression and hindlimb paralysis, but tumors progressed in the other mice in those groupsas well as in non-treated mice. These non-responding animals did notexhibit signs of myositis and were euthanized when their tumors weregreater than 10 percent of body weight.

TABLE 7 Mean virus titers in mouse serum/group (TCID₅₀). RNA (μg) 3 day7 day 10 day 14 day 17 day 21 day 0 0 0 0 0 0 0  1 5e2 6e4 1e5 6e4 0 0**2 5e2 0 1e6 6e4 8e4  8e4  4 1e6 1e6 6e6 1e6 7e5  3e5** 8 2e6 7e4 7e4 1e63e4** 3e4** 16 2e4 6e5 8e5  3e5** 3e4** 0** 32 6e4 2e5 1e6 1e5 3e6****Denotes more than 50% of mice dead in group

In another study, two mice bearing myeloma xenografts were tested todetermine whether CVA21 infectious RNA given intravenously initiates theoncolytic intratumoral CVA21 infection. Two SCID mice bearing KAS6/1subcutaneous xenografts were each given an intravenous tail veininjection of a solution containing 50 μg CVA21 RNA. By day 4 postinjection of the RNA, both mice had measurable viral titers in theirserum (TCID₅₀=3×10⁵ per mL). In addition, tumor regression began aroundday 7 with hind limb paralysis at day 9 followed by death at day 10 withserum virus titers at 3×10⁶ TCID₅₀ (Table 8 and FIG. 5).

TABLE 8 Progression of infection in mice treated intravenously withinfectious viral RNA. Day 4 serum Tumor Hind limb Death (Serum TCID₅₀regression paralysis TCID ₅₀) Mouse 1 3e5 Day 8 Day 10 Day 11 Mouse 23e5 Day 6 Day 10 Day 11 (3e6)

Example 6 microRNA-Dependent Silencing in Muscle

A microRNA-dependent technique for controlling viral gene expression wasdeveloped to control effects associated with viral expression innon-tumor cells (e.g., myositis associated with CVA21 therapy).Coxsackievirus A21, a picornavirus with a 7.4 kb genome, is not wellsuited for the incorporation of trackable transgenes. Therefore, to testthe ability of microRNA target elements to confer tissue-specificsilencing of a virus in vitro, GFP-tagged plasmids and lentiviralvectors expressing GFP were generated. Three highly conserved,muscle-specific microRNAs (miR-1, miR-133, and miR-206) were selected aspotential modulators of gene expression, and target elementscomplementary to these microRNA sequences were incorporated into the3′UTR of GFP. Immunofluorescence and flow-cytometric analysis revealedmicroRNA target element-dependent suppression of gene expression in themuscle cells, while controls with hematopoetic cell-specific microRNAtarget elements remained unaffected. Induction of higher levels ofmiR-1, miR-133, and miR-206 in muscle cells amplified this effect. Theseresults demonstrate that the incorporation of microRNA target elementsinto the viral genome provides an effective approach by which tissuetropism of oncolytic viruses can be altered.

Materials and Methods

Cell culture, transfections, and lentiviral vector production. HeLa, L6,TE-671, C2C12, 293T, and 3T3 cells were obtained from American TypeCulture Collection and were maintained in DMEM supplemented with 10% FBS(also referred to as Growth Medium) in 5% CO₂. Cells were differentiatedin DMEM supplemented with 2% horse serum for four days. Transfectionswere performed using the Promega (Madison, Wis.) Calcium PhosphateProFection mammalian Transfection System with a total of 3 μg of DNA perwell in a six-well plate. Briefly, cells were transfected at 24 hoursafter being plated in 2 mL of medium at 0.25×10⁶ cells/well. Cells wereharvested or used for immunofluorescence 72 hours after transfection.Lentiviral vectors were obtained by transfection of 10 μg of eachlentiviral transfer plasmid (pHR-sin-CSGW dlNot1 or pHR-sin-F.Luc)provided by Y. Ikeda and lentiviral packaging plasmid (CMV ΔR8.91), and3 μg VSV-G packaging construct pMD.G in a T75 flask. Supernatant washarvested at 72 hours post transfection, and filtered through a 0.45micron syringe filter.

Plasmid Construction.

microRNA sequences were obtained from the Sanger Institute miRBasedatabase (internet site “microrna.sanger.ac.uk/sequences/”). Oligos wereannealed in equimolar amounts in STE Buffer by heating to 94° C.followed by gradual cooling at bench top. Oligos were designed usingmethods described elsewhere (Brown et al., Nat. Med., 12:585-591(2006)). The following oligos were used for annealing. The underlinedsequences represent microRNA target elements. The annealed oligos werecloned into XhoI/NotI site of pHR-sin-CSGW dlNot1, and lentiviralvectors were produced.

Briefly, four tandem copies of target elements for miR-133 and miR206were incorporated into the 3′UTR of the lentiviral vector. Ahematopoetic cell-specific microRNA target element for miR142-3P wasincorporated in the same fashion and used as a control. Two furtherconstructs were generated incorporating two tandem copies of twomuscle-specific microRNA target elements (miR1 and miR-133 to formconstruct miR1/133T, and miR133 and 206 to form miR133/206T; FIG. 6A).

miR133 Sense #1: (SEQ ID NO: 1)5′-GGCCGCACAGCTGGTTGAAGGGGACCAACGATACAGCTGGTTG AAGGGGACCAAACCGGT-3′Sense #2: (SEQ ID NO: 2) 5′-ACAGCTGGTTGAAGGGGACCAATCACACAGCTGGTTGAAGGGGACCAAC-3′ Anti-sense #1: (SEQ ID NO: 3)5′-TTGGTCCCCTTCAACCAGCTGTATCGTTGGTCCCCTTCAACCA GCTGTGC-3′ Anti-sense #2:(SEQ ID NO: 4) 5′-TCGAGTTGGTCCCCTTCAACCAGCTGTGTGATTGGTCCCCTTCAACCAGCTGTACCGGT-3′ miR206 Sense #1: (SEQ ID NO: 5)5′-GGCCGCCCACACACTTCCTTACATTCCACGATCCACACACTTC CTTACATTCCAACCGGT-3′Sense #2: (SEQ ID NO: 6) 5′-CCACACACTTCCTTACATTCCATCACCCACACACTTCCTTACATTCCAC-3′ Anti-sense #1: (SEQ ID NO: 7)5′-TGGAATGTAAGGAAGTGTGTGGATCGTGGAATGTAAGGAAGTG TGTGGGC-3′ Anti-sense #2:(SEQ ID NO: 8) 5′-TCGAGTGGAATGTAAGGAAGTGTGTGGGTGATGGAATGTAAGGAAGTGTGTGGACCGGT-3′ miR1/133 Sense #1: (SEQ ID NO: 9)5′-GGCCGCTACATACTTCTTTACATTCCACGATTACATACTTCTT TACATTCCAACCGGT-3′Sense #2: (SEQ ID NO: 10) 5′-ACAGCTGGTTGAAGGGGACCAATCACACAGCTGGTTGAAGGGGACCAAC-3′ Anti-sense #1: (SEQ ID NO: 11)5′-TGGAATGTAAAGAAGTATGTAATCGTGGAATGTAAAGAAGTAT GTAGC-3′ Anti-sense #2:(SEQ ID NO: 12) 5′-TCGAGTTGGTCCCCTTCAACCAGCTGTGTGATTGGTCCCCTTCAACCAGCTGTACCGGT-3′ miR133/206 Sense #1: (SEQ ID NO: 13)5′-GGCCGCACAGCTGGTTGAAGGGGACCAACGATACAGCTGGTTG AAGGGGACCAAACCGGT-3′Sense #2: (SEQ ID NO: 14) 5′-CCACACACTTCCTTACATTCCATCACCCACACACTTCCTTACATTCCAC-3′ Anti-sense #1: (SEQ ID NO: 15)5′-TTGGTCCCCTTCAACCAGCTGTATCGTTGGTCCCCTTCAACCA GCTGTGC-3′ Anti-sense #2:(SEQ ID NO: 16) 5′-TCGAGTGGAATGTAAGGAAGTGTGTGGGTGATGGAATGTAAGGAAGTGTGTGGACCGGT-3′ miR142-3p Sense #1: (SEQ ID NO: 17)5′-GGCCGCTCCATAAAGTAGGAAACACTACACGATTCCATAAAGT AGGAAACACTACAACCGGT-3′Sense #2: (SEQ ID NO: 18) 5′-TCCATAAAGTAGGAAACACTACATCACTCCATAAAGTAGGAAACACTACAC-3′ Anti-sense #1: (SEQ ID NO: 19)5′-TGTAGTGTTTCCTACTTTATGGAATCGTGTAGTGTTTCCTACT TTATGGAGC-3′Anti-sense #2: (SEQ ID NO: 20)5′-TCGAGTGTAGTGTTTCCTACTTTATGGAGTGATGTAGTGTTTC CTACTTTATGGAACCGGT-3′

Luciferase Assays and Flow Cytometry.

2.5×10⁵ cells were plated in 6 well plates with DMEM+10% FBS andinfected with HIV-based lentiviral vectors containing a luciferase gene.72 hours post transfection, half of the cells were harvested for flowcytometry, and the remaining half were used for a luciferase assay. Forthe luciferase assay, cells were lysed in 1 percent triton-X 100 in PBS.Luciferase levels were quantified using the TopCount microplateluminescence counter. Cells for flow cytometry were fixed in 4 percentparaformaldehyde in PBS, washed, and resuspended in PBS+2 percent FBS,and GFP was quantified using a Becton Dickinson FACScan flow cytometer.Flow data was analyzed using the BD CellQuest Software.

Results

Muscle microRNA Target Element Incorporation Suppresses TransgeneExpression in Muscle Cells.

A total of five cell lines were used to test the constructed microRNAtarget element-tagged lentiviral vectors. The human cell lines H1-HeLaand 293T, along with the mouse cell line 3T3 were used as controls asthey are not of muscle origin, while the human rhabdomyosarcoma lineTE671 and the rat myoblast line L6 were used as muscle cells expressingmiR-1, miR-133, and miR-206 (Anderson et al., Nucleic Acids Res.,34:5863-5871 (2006)). Cell lines were transduced with lentiviral vectorsexpressing muscle or control microRNA target elements in the 3′UTR ofGFP and a control containing a non-tagged luciferase encoding vector(FIG. 6B). Flow cytometry analysis revealed marked inhibition of GFPexpression specifically in muscle cells in vectors containing targetelements for miR-206 and a combination of target elements of bothmiR-133 and miR-206. Luciferase assay results indicated that this effectwas directed only towards those transgenes containing muscle-specificmicroRNA target elements as luciferase expression remained constant inall cells (FIGS. 7, 9, and 10-18).

Increased microRNA Expression Results in Increased microRNA TargetElement-Mediated Suppression.

To determine if the microRNA-mediated silencing can be enhanced by amore robust expression of muscle specific microRNAs, cells were culturedin the presence of differentiation medium, which can increase expressionof muscle-specific microRNAs (Anderson et al., Nucleic Acids Res.,34:5863-5871 (2006)). By increasing the expression of microRNAs, thenumber of RNA-Induced Silencing Complexes (RISCs) is potentially greatlyincreased as is the potential for overcoming the effect of saturation ofthe microRNA pathway, should such a saturation occur. When cultured inthe absence of FBS and in the presence of horse serum, microRNA-mediatedsilencing of GFP expression increased by about 1.5 and 3 fold in TE671and L6 cells, respectively (FIGS. 8 and 9).

Taken together, the results provided herein demonstrate that targetelements for tissue-specific microRNAs can be incorporated into viralnucleic acid to control virus stability, viral replication, and viralgene expression. By incorporating target elements for tissue-specificmicroRNAs into the genome of a virus, one can modulate the stability ofnot only viral transcripts, but also the actual template from whichtranscripts are derived.

Example 7 microRNA Regulated CVA21

MicroRNAs are emerging as new potent and active cellular regulators. Toshow that naturally occurring and differentially expressed miRNAs can beexploited to modulate the tropism of a replicating virus, anmiRNA-regulated CVA21 was constructed. Two copies each of the targetsequences coding for miR-133 and miR-206 were inserted in the 3′NTR ofCVA21.

Materials and Methods

Recombinant CVA21 Construction.

The following sequences were cloned into the 3′NTR of pGEM-CVA21(obtained from Matthias Gromeier) in between by 7344/7345 by overlapextension PCR. As indicated above, miR-142 3pT is a hematopoeitic cellspecific control, while miR133T, miR206T, miR 133/206T are musclespecific.

(miR-142 3pT) (SEQ ID NO: 80)TCCATAAAGTAGGAAACACTACACGATTCCATAAAGTAGGAAACACTACACTGGAGTCCATAAAGTAGGAAACACTACATCACTCCATAAAGTA GGAAACACTACA (miR 133T)(SEQ ID NO: 81) ACAGCTGGTTGAAGGGGACCAACGATACAGCTGGTTGAAGGGGACCAACTGGAGACAGCTGGTTGAAGGGGACCAATCACACAGCTGGTTGAAG GGGACCAA (miR 206T)(SEQ ID NO: 82) CCACACACTTCCTTACATTCCACGATCCACACACTTCCTTACATTCCACTGGAGCCACACACTTCCTTACATTCCATCACCCACACACTTCCTT ACATTCCA (miR 133/206T)(SEQ ID NO: 83) ACAGCTGGTTGAAGGGGACCAACGATACAGCTGGTTGAAGGGGACCAACTGGAGCCACACACTTCCTTACATTCCATCACCCACACACTTCCTT ACATTCCA

Virus and Viral RNA Production.

Viral RNA was produced using Ambion Megascript and Megaclear T7polymerase kit according to the manufacturer's instructions. One μgRNA/well was transfected into H1-HeLa cells in 12 well plates using theMinis (Madison, Wis.) TranIT®-mRNA transfection reagent. Afterincubating for 24 hours, wells were scraped and cell pellets harvested.Cell pellets were subjected to three freeze/thaw cycles in liquid N2,cell debris was cleared by centrifugation, and the resulting clearedlysate was added to H1-HeLa cells in a T-75 flask. For CVA21 miRT, threepassages were required to obtain suitable titers of virus.

CVA21 Titration.

Titration of CVA21 was performed on H1-HeLa cells. Cells were plated in96 well plates at 50% confluence. After 24 hours, serial ten-folddilutions (−2 to −10) were made of the virus; 100 μL of each dilutionwere added to each of eight duplicate wells. Following incubation at 37°C. for 72 hours, wells were fixed and stained (0.1% crystal violet, 20%methanol, 4% paraformaldehyde). Wells then were assessed for CPEmanifest as non-staining areas devoid of viable cells. If purplestaining cells were seen on 75% or less of the well surface, then thewell was scored positive. TCID₅₀ values were determined using theSpearman and Kärber equation.

One Step Growth Curves.

Each cell line was incubated with CVA21 at a MOI (multiplicity ofinfection) of 3.0 for 2 hours at 37° C. Following this incubation, cellswere centrifuged, and unincorporated virus was removed. Cells wereresuspended in fresh growth media at predetermined time-points (2, 4, 6,18, 12, 24, hours), cells pellets were harvested and frozen at −80° C.At the completion of all time-points, the cell pellets were thawed. Celldebris was cleared from each cell pellet by centrifugation to provide acleared cell lysate fraction.

miRNA Mimics.

miRNA mimics were purchased from Dharmacon, Inc. (Lafayette, Colo.). Thecontrol miRNA mimic corresponded to a C. elegans miRNA with no predictedmiRTs in mammalian cells. miRNA mimics were transfected with MirusTranIT®-mRNA transfection reagent at a 200 nM concentration. Four hourspost mimic transfection, cells were infected with WT, miRT, or RevTCVA21 at MOI=1.0. After 24 hrs. post infection, cells were harvested foran MTT viability assay and supernatant was harvested for titration.

In Vivo Experiments.

CB17 ICR-SCID mice were obtained from Harlan (Indianapolis, Ind.). Micewere irradiated and implanted with 5e6 Kas 6/1 or Mel 624 cells in theright flank. When tumors reached an average of 0.5×5 cm, tumors weretreated with 1e6 CVA21. Tumor volume was measured using a hand heldcaliper and blood was collected by retroorbital bleeds. Histological andpathological analysis of mice was performed by Mayo Clinic ScottsdaleResearch Histology after terminal perfusion with 4% paraformaldehyde.

Results

Two copies each of the target sequences coding for miR-133 and miR-206were inserted in the 3′NTR of CVA21 (see FIG. 33A). The miRT virus wasrescued by RNA transfection in H1-HeLa cells and its replicationkinetics were compared with those of the parental WT strain of CVA21. Asshown in FIGS. 33B, 33C and 33D, the growth kinetics of these twoviruses are indistinguishable on H1-HeLa, Mel-624 and Kas 6/1 cells anddid not differ from the growth of a control virus (RevT) carrying acontrol insert in the 3′NTR (see below).

To determine whether the lytic effects of the miRT CVA21 recombinantvirus could be controlled by muscle-specific miRNAs, CVA21-susceptibleH1-HeLa cells were infected with test and control viruses (moi=1.0)after first transfecting them with microRNA mimics corresponding tomiR-133, 206, or with a control mimic corresponding to a C. elegansmiRNA that has no identified target in mammalian cells. Mimics ofmiR-133 or miR-206 each partially protected the H1-HeLa cells from virallysis by miRT CVA21 with miR-206 providing greater protection thanmiR-133. When cells were exposed simultaneously to both of the musclespecific miRNA mimics, they appeared to be fully resistant to theretargeted virus such that cell viability was not significantlydifferent from mock infected cells (p=0.49) (FIG. 33F).

To determine whether propagation of the miRT CVA21 virus was efficientlyblocked by the muscle-specific microRNAs in a sequence-specific manner,the supernatant virus titers also were measured in this experiment.Virus titers in the supernatants of cells infected with miRT CVA21 weresubstantially decreased by miR-133 (two log reduction) or miR-206 (threelog reduction) when the mimics were applied individually, but weredecreased to undetectable levels (>five log reduction) in the presenceof both muscle-specific mimics (FIG. 33G). It also was confirmed thatcells could be significantly protected by endogenously encoded miRNAs bytransfecting infectious RNA for WT and miRT CVA21 in H1-HeLa or themuscle cell line TE-671. As shown in FIG. 33H, endogenously encoded andexpressed miRNAs significantly protected muscle cells from cytopathiceffects of miRT CVA21 (p<0.01).

To investigate if miRT CVA21 retained oncolytic in vivo efficacy and ifit provided a protection phenotype against fatal myositis,immunodeficient mice carrying subcutaneous xenografts derived from humanmyeloma or melanoma cell lines were infected (FIG. 34A-C, FIG. 35A-D,FIG. 36A-C). Mice carrying established subcutaneous tumors were treatedwith a single intratumoral dose of 10⁶ TCID₅₀ of each virus andmonitored for tumor growth and survival. WT treated animals had quickand in some cases complete tumor regression, but all developedgeneralized muscle paralysis and were euthanized in less than 15 days.Animals treated with the miRT virus, however, had slow but eventuallycomplete tumor regression and significantly increased survival ascompared to WT treated animals (FIG. 34D) (p<0.001).

Histological analysis of muscle tissue in mice treated with WT virusagain showed massive infiltration and necrosis while animals treatedwith miRT virus were rescued from this phenotype. Though survival wasstatistically significant (p<0.001 vs control and WT CVA21), a smallnumber of mice developed tremors and labored breathing and, in 2 cases,paralysis and were euthanized (FIG. 34D). Pathologic examination ofthese mice indicated that this was symptomatic of a polio-like myelitisrather than myositis. To determine if this was caused by a persistantviremia that may have allowed a retrograde axonal transport of the virusto occur, viral titers present in mouse serum were examined.

Serum collected from all mice was analyzed at two-week intervals afterCVA21 treatment. Mice treated with miRT CVA21 had initial high levelviremia, consistent with the viremia seen in WT CVA21 treated animals(FIG. 34F). In some animals, this viremia persisted enabling theanalysis of the stability of the miRT insert. Though RNA interferenceagainst vertebrate viruses is not generally accepted as naturallyoccurring by microRNA targets encoded within viral genomes, the resultsshow that engineered microRNA targets in viruses are capable ofregulation by miRNA primed RNAi machinery.

To the essence of whether vertebrate viruses evolved to avoid miRTswithin their viral genomes and to test if insertion of miRTs can providea long-term means of targeting, stability of the insertions was examined45 days after virus administration (FIG. 34G). Because of the nature ofthe replication cycles of both Kas 6/1 myeloma cells and CVA21, there isan assurance of a high amount of viral turnover. This, combined with thehigh error rate of RNA-dependent RNA polymerases provided opportunityfor the virus to mutate the inserted sequence. In animals that hadviremia, 6/11 animals maintained 100% sequence identity with theoriginal sequence; 3 animals had >80% sequence homology with theinserted miRTs, 1 animal retained only 68% of the inserted target, andone animal had limited sequence retention (RevT). All animals maintainedperfect homology in the flaking 3D_(pol) and 3′NTR sequence to the WTvirus. Though there was a significant amount of target retention in thisexperiment, the terminal point in this study was 70 days, at which pointthe major substrate for viral replication (hsICAM-1 positive Kas 6/1cells) in mice was no longer present.

To address the possibility that the altered in vivo host rangeproperties of the miRT virus might be a nonspecific consequence ofplacing a 100 base insert into its 3′UTR, the RevT virus (so calledbecause of the revertant phenotype it displayed in mice) wascharacterized. This virus carries a 3′NTR insert with the identicalinsertion site to the microRNA targeted virus, but retains only minimalhomology to the original microRNA target sequence (FIG. 37B). The RevTinsert was cloned into the lentiviral GFP reporter vector (FIG. 37A) anddemonstrated that it was unable to mediate muscle cell-specificsilencing of lentiviral gene expression (FIG. 37C). Finally, the RevTvirus was administered by intratumoral inoculation to mice bearing largesubcutaneous KAS6/1 myeloma xenografts, at the same time treatingcontrol groups of mice with the wild type and microRNA retargetedviruses. As shown in FIG. 34E and FIG. 35, the in vivo behavior of theRevT virus was indistinguishable from that of the wild type virus. AllRevT-challenged animals died within 14 days of virus administration fromsevere, generalized myositis. These in vivo results confirm and extendthe conclusion of the in vitro studies: that the host range of apathogenic RNA virus can be controlled by cellular microRNAs.

Other Embodiments

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

What is claimed is:
 1. A method for treating cancer present in a mammal,wherein said method comprises administering, to said mammal, aneffective amount of nucleic acid coding for a picornavirus underconditions wherein cancer cells present within said mammal undergo celllysis as a result of synthesis of picornavirus from said nucleic acid,thereby reducing the number of viable cancer cells present within saidmammal.